Selecton: a server for detecting evolutionary forces at a single amino-acid site

Doron‐Faigenboim, Adi; Stern, Adi; Mayrose, Itay; Bacharach, Eran; Pupko, Tal

doi:10.1093/bioinformatics/bti259

Cited by 134 publications

(118 citation statements)

References 20 publications

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“…Such variability is likely to be advantageous to the organism [42]. Positive and negative selection pressure at each site was estimated by the ratio of nonsynonymous (K a ) substitutions to synonymous substitutions (K s ), namely the K a /K s ratio.…”

Section: Synteny Analysis Of the P2x Genes In Vertebratesmentioning

confidence: 99%

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Comparative study of the P2X gene family in animals and plants

Hou

Cao

2016

Purinergic Signalling

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P2X receptors are ligand-gated ion channels that can bind with the adenosine triphosphate (ATP) and have diverse functional roles in neuropathic pain, inflammation, special sense, and so on. In this study, 180 putative P2X genes, including 176 members in 32 animal species and 4 members in 3 species of lower plants, were identified. These genes were divided into 13 groups, including 7 groups in vertebrates and 6 groups in invertebrates and lower plants, through phylogenetic analysis. Their gene organization and motif composition are conserved in most predicted P2X members, while groupspecific features were also found. Moreover, synteny relationships of the putative P2X genes in vertebrates are conserved while simultaneously experiencing a series of gene insertion, inversion, and transposition. Recombination signals were detected in almost all of the vertebrates and invertebrates, suggesting that intragenic recombination may play a significant role in the evolution of P2X genes. Selection analysis also identified some positively selected sites that acted on the evolution of most of the predicted P2X proteins. The phenomenon of alternative splicing occurred commonly in the putative P2X genes of vertebrates. This article explored in depth the evolutional relationship among different subtypes of P2X genes in animal and plants and might serve as a solid foundation for deciphering their functions in further studies.

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Section: Synteny Analysis Of the P2x Genes In Vertebratesmentioning

confidence: 99%

“…These models use different biological assumptions testing the model that better fits the data. The models are Bayesian models that assume a statistical distribution to account for heterogeneous K a /K s values among sites and the number of categories for the distribution is 8 as the default value [42].…”

Section: Synteny Analysis Of the P2x Genes In Vertebratesmentioning

confidence: 99%

Comparative study of the P2X gene family in animals and plants

Hou

Cao

2016

Purinergic Signalling

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“…First, we ran the data on the Selecton Server (Doron-Faigenboim et al 2005;Stern et al 2007). LRTs were conducted between the M8 model (b and x s C 1), which enables positive selection, and the M8a (b and x s = 1; no positive selection) and M7 (only purifying selection) models.…”

Section: Molecular and Phylogenetic Analysesmentioning

confidence: 99%

Molecular Characterization of Two Endothelin Pathways in East African Cichlid Fishes

Diepeveen

Salzburger

2011

J Mol Evol

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The adaptive radiations of cichlid fishes in East Africa have been associated with the acquisition of evolutionary novelties as well as the ecological opportunities existing in the East African Great lakes. Two remarkable evolutionary innovations are the pharyngeal jaw apparatus, found in all cichlid species, and the anal fin egg-spots of mouthbrooding cichlids. Based on their conserved functions during the development of both the jaw apparatus and pigmentation, the endothelin ligands and receptors form a putative link between these naturally and sexually selected traits. Here we study the evolutionary history of four members of two endothelin pathways (Edn1/EdnrAa and Edn3b/EdnrB1a) to elucidate their possible roles during the evolution and development of key innovations in East African cichlids species. The analyses performed on partial sequences (ca. 6,000 bp per taxon) show that all four endothelin family members evolved under purifying selection, although both ligands are characterized by an accelerated rate of protein evolution in comparison to the receptors. In accordance with earlier findings, we show that the mature protein sequence of Edn1 and Edn3 are highly conserved, also in cichlids, whereas the preproendothelin parts are variable indicating relaxed selective constraints. In the receptors, nonsynonymous substitutions were mainly found in the ligand-binding domains suggesting functional divergence. Gene expression assays with Real-Time PCR indeed reveal that the two studied endothelin pathways are expressed in the cichlid pharyngeal jaw and in the haplochromine egg-spot (among other pigment-cell containing tissues), suggesting their involvement during morphogenesis of naturally and sexually selected traits in cichlids.

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“…Important conserved regions are the active site residues 22 -34, the flap loop residues 47 -52 which control access to the active site, and a region containing an α-helix and part of the hydrophobic core residues 74 -87. [38] The dynamic localization is represented in Figure 3 by projecting the mode amplitudes along the protein sequence, and making the radius and color of the tube rendering directly proportional to the extent of the local mode fluctuation the position inside the primary sequence of the large-amplitude internal modes shows that the slow modes are mostly localized along the flap loop and the terminal region. This is consistent with the role of the flap loop in HIV protease, mediating access to the active site.…”

Section: A Hiv Proteasementioning

confidence: 99%

Mode localization in the cooperative dynamics of protein recognition

Copperman

Guenza

2016

The Journal of Chemical Physics

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The biological function of proteins is encoded in their structure and expressed through the mediation of their dynamics. Local fluctuations are known to initiate biologically relevant pathways as they cooperatively enhance the dynamics in specific regions in the protein. Those biologically active regions provide energetically-comparable conformational states that can be trapped by a reacting partner. We analyze this mechanism as we calculate the dynamics of monomeric and dimerized HIV protease, and free Insulin Growth Factor II Receptor (IGF2R) domain 11 and its IGF2R:IGF2 complex. We adopt a newly developed coarse-grained model, the Langevin Equation for Protein Dynamics (LE4PD), which predicts dynamical relevant mechanisms with high accuracy. Both simulation-derived and experimental NMR conformers are the input structural ensembles for the LE4PD. The use of the experimental NMR conformers requires minimal computational resources.

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Selecton: a server for detecting evolutionary forces at a single amino-acid site

Abstract: More information is available at http://selecton.bioinfo.tau.ac.il/overview.html. A set of examples is available at http://selecton.bioinfo.tau.ac.il/gallery.html.

Cited by 134 publications

References 20 publications

Comparative study of the P2X gene family in animals and plants

Comparative study of the P2X gene family in animals and plants

Molecular Characterization of Two Endothelin Pathways in East African Cichlid Fishes

Mode localization in the cooperative dynamics of protein recognition

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